In January 1940, 801 NAS was based at RNAS Donibristle with the Blackburn Skua, playing a key role in the early part of the war with operations in Norway while deploying from the aircraft carrierHMS Ark Royal. In September, 801 Squadron embarked on Furious for raids on the northerly parts of the Norwegian coast. Following an attack on Trondheim on 22 September, Skua L2942 piloted by Sub-Lieutenant Bernard Wigginton with Leading Aircraftman Kenneth King as his gunner, was unable to find their carrier and crash landed in neutral Sweden.

In 1943 880 Naval Air Squadron formed the 30 Naval Fighter Wing on HMS Implacable. In June 1945, naval fighter wings were reformed as carrier groups with 801 NAS, 828 NAS, 880 NAS and 1771 NAS becoming the 8th Carrier Air Group. In August 1941 they re-equipped with Sea Hurricanes at RNAS Yeovilton, Captain George Clifton Baldwin commanded the station from 1966-1968) The squadron deployed to the Mediterranean aboard Argus, then to Eagle. During this deployment 801 NAS claimed thirteen enemy aircraft of various types, for the loss of three Hurricanes and four Fulmars. Two of the Fulmars were brought down by friendly fire.

In March 1951, 801 NAS received Hawker Sea Furys and the squadron saw active service during the Korean War flying from Glory. Glory was deployed in theatre from 3 April 1951 to 30 September 1951 and from 8 November 1952 to the Korean Armistice Agreement of 27 July 1953. 801 NAS was embarked on the second tour of duty.

Sea Furies could be armed with either two bombs or four rockets and drop tanks in both cases. The aircraft were mainly used in the ground attack role armed with bombs and rockets, but they were also engaged in air-to-air combat with the much faster MiG-15.

On 18 March 1962, 801 squadron was reformed at Lossiemouth in the strike role with Buccaneers. In July 1962 they embarked 10 aircraft in Victorious for the Far East. The squadron subsequently received the 1967 Boyd Trophy, an annual award for the best squadron in the Fleet Air Arm, for its efforts in bringing the Buccaneer into service.

801 transferred to Hermes with 7 aircraft in 1968 for a further spell in Eastern waters. In March 1969 the ship returned home to spend the next year in Home and Mediterranean waters. The squadron eventually disbanded at Lossiemouth on 21 July 1970.

1 May 1982 - A Mirage III of FAA Grupo 8 shot down north of West Falkland by Barton using a Sidewinder. The Argentine pilot ejected.

1 May 1982 - A Mirage III of FAA Grupo 8 damaged in same incident north of West Falkland by Thomas using a Sidewinder air-to-air missile. The Mirage was then shot down over Stanley by Argentine anti-aircraft defences killing the pilot.

1 May 1982 - A Canberra B62 of FAA Grupo 2 was shot down north of Falklands by Curtis using a Sidewinder. The Argentine pilots ejected but were not rescued.

21 May 1982 - A Pucará of FAA Grupo 3 was shot down near Darwin by Ward in one of three Sea Harriers using 30 mm cannon fire. The pilot ejected from the aircraft at about 40 ft above the ground, he survived and walked back to Goose Green.[7][8]

21 May 1982 - Three Dagger As of FAA Grupo 6 were shot down north of Port Howard, West Falkland using Sidewinders, two by Thomas and the other by Ward. All three Argentine pilots successfully ejected.

1 June 1982 - A C-130E Hercules of FAA Transport Grupo 1 was shot down 50 miles north of Pebble Island by Ward using two AIM-9 Sidewinders and cannon. The crew of seven were killed.

6 May 1982 - Two aircraft collided in bad weather while flying a night sortie south east of East Falkland, investigating a radar contact close to the burnt-out wreck of HMS Sheffield. Both pilots were killed and no trace of either aircraft found.

29 May 1982 - A Sea Harrier was being made ready for take-off, and slid off the deck when Invincible turned sharply into the wind. The pilot ejected, and was picked up.

Lieutenant Commander Ward and Lieutenant Thomas were each awarded the Distinguished Service Cross for their conduct and leadership throughout the campaign.
Lieutenant Commander Kent and Flight Lieutenant Mortimer were both Mentioned in Despatches. Lt Curtis was posthumously Mentioned in Despatches

On Tuesday 28 March 2006 a ceremony was held at RNAS Yeovilton, with Commander A J W Rae as the last Sea Harrier squadron commanding officer, to mark the withdrawal from service of the Royal Navy's Sea Harrier FA2s. The final Sea Harrier was withdrawn from service on 31 March 2006 at RNAS Yeovilton and the squadron disbanded. Prior to decommissioning, all aircraft adopted the omega symbol on their tail-fin in recognition of 801 NAS being the last operators of an all-British fixed-wing fighter aircraft. This harks back to the use of this symbol by 892 Naval Air Squadron, whose McDonnell Douglas Phantom FG.1s were the last conventional fixed-wing aircraft used by the Fleet Air Arm.

801 NAS was due to recommission in March 2007, under the command of Commander K Seymour, to operate the Harrier GR7 and GR9 from RAF Cottesmore. However, due to lack of manpower all former 801 and 800 NAS (their sister squadron) personnel formed a "Naval Strike Wing" within RAF Cottesmore, thus severing all remaining ties to their former home at RNAS Yeovilton.[10] On 1 April 2010, Naval Strike Wing reverted to the identity of 800 Naval Air Squadron.[11]